Biology is defined as the study of life / living things. A living thing is defined as anything that converts energy from one form to another, while using that energy to grow, change, and reproduce.
The scientific method is the standard guideline for discovery and experimentation in the sciences (chemistry, physics, biology, etc..) The basic steps are...
The last step (refine and iterate) just means that you do it all over again but make changes based on the things you learned from your experiment. For example, ...
The scientific method revolves around making an observation and coming up with a testable explanation for that observation -- called a hypothesis. If the explanation isn't testable, you can't consider it a hypothesis. For example, a good hypothesis may be that increased sun exposure leads to an increased risk of skin cancer because it's something you can test. A bad explanation may be that exposure to centaurs increase the risk of skin cancer because centaurs don't exist (and as such the hypothesis can't be tested).
Once you have a hypothesis, you design an experiment to test it. In the case of our sun exposure leads to increased risk of skin cancer hypothesis, an experiment may be to expose skin cells to UV rays in amounts equivalent to that given off by the sun and then check to see if those cells have been damaged (compared to a control group of skin cells that you haven't exposed to UV rays).
What makes a good experiment?
Other terminology around the scientific method...
An element is matter that cannot be broken down any further by chemical reaction -- it's a substance made entirely out of one type of atom. Each element/atom has a specific set of properties that defines how it acts/reacts (e.g. weight, colour, how light reflects, etc..).
Examples of elements/atoms:
Examples of non-elements:
The building blocks of atoms are protons, neutrons, and electrons. Protons and neutrons form the nucleus of the atom while electrons jump around outside of the nucleus. Protons and electrons are attracted to each other -- protons are positively charged while electrons are negatively charged. Although, protons and electrons never fully meet (electrons are always buzzing/hovering around the outside of the nucleus where the protons are).
The configuration of an atom (protons/neutrons/electrons) is what allows us to predicate how one element may react to another element. For example, certain elements may attract, repel, bond, swipe electrons, etc..
The number of protons are what defines the type of atom/element. For example, hydrogen has 1 proton, helium as 2, lithium has 3, etc.. The number of neutrons and electrons can change without changing the type of element as long as the number of protons remain the same.
The periodic table below orders elements/atoms by the number of protons (also called the atomic number)...
When atoms bind together, they form a molecule. Each type of molecule has the same configuration of atoms -- same atoms in the same numbers, structured/shaped similarly. For example, a water molecule is made up of 2 hydrogen atoms and 1 oxygen atom binding together in a house-roof shape...
A monomer is a special designation for atoms/molecules that are able to join with other monomers to create even larger molecules. The process of joining is called polymerization and the resulting molecule is called a polymer.
If the monomers that make up a polymer are all the same, the polymer is called a homopolymer. Otherwise, it's called a heteropolymer / copolymer.
For example, the glucose molecule is a monomer. It can combine with other glucose molecules to create the glycogen molecule, which is a polymer / homopolymer. Other examples of polymers (according to Wikipedia): amino acids and nucleotides (DNA).
Polymers are often referred to as macromolecules -- molecules that have a very large number of atoms.
An ion is a charged atom or molecule. A charged atom/molecule just means that it has an unequal number of protons and electrons:
Ions are always trying to lose their charge and become neutral, either by giving up an electrons or pulling in an electrons such that the the number of protons and electrons become equal. As such, ions will attract towards oppositely charged ions and repel from similarly charged ions:
pH stands for potential of hydrogen and it's the measure of positively charged hydrogen ions in a solution. The more...
pH is scaled logarithmically from 1 to 14. Each notch on the scale moves the acidity/basicity by a factory of 10. Going...
For example, going from 7 to 4 increases acidity by 1000x times / decreases basicity by 1000x.
The closer to...
Carbohydrates (also called saccharides) are molecules that consist of a mix of carbon, hydrogen, and oxygen atoms. In biological systems, carbohydrates are often associated with...
The term monosaccharide is just means a carbohydrate that's a monomer (e.g. glucose). Similarly, the term polysaccharide means a carbohydrate built from other monosaccharides (e.g. glycogen is made of chained glucose).
Proteins are molecules that consist of monomers called amino acids. The amino acids get chained together into a polymer called a polypeptide chain, and one or more polypeptide chains fold to a 3D structure and combine to become a protein. The 3D structure / shape of the protein (how its folded) is what gives it its abilities.
In biological systems, proteins are often associated with that facilitating some biological function. For example, the protein protease is responsible for breaking down food.
The basic structure of an amino acid is as follows. The R is a placeholder that, when set, defines what type of amino acid it is...
Lipids are molecules that are somewhat not water soluble -- meaning that they have parts that resist water but maybe also parts that are attracted to water. In biological systems, lipids are often associated with...
Nucleic Acid is a molecule (heteropolymer) often associated with information storage. It's built up from other molecules called {bm} nucleotides (monomers). It's called nucleic acid because it's in the nucleus of a cell and it has some acidic properties to it.
Deoxyribonucleic acid (DNA) is the most common form of nucleic acid. DNA is a molecule that contains the instructions needed for the growth/functioning/maintenance of an organism. Depending on the type of organism, DNA is located either in the cell’s nucleus (for eukaryotic organisms -- animals and plants) or the cell’s cytoplasm (for prokaryotic organisms -- single-celled organism).
Ribonucleic acid (RNA) is another common form of nucleic acid. RNA is a molecule used as a transferring mechanism for copying over information from DNA to other cellular machinery. It's also used as information storage for (some?) viruses.
The monomers that make up nucleic acid molecule are called nucleotides, and the order they appear in defines the genetic information/instructions.
There are 5 different nucleotides:
The order the appear in defines the genetic information/instructions of that organism. Because they are the unit by which genetic information is encoded, each nucleotide is also called a base. For example, a string/sequence of DNA bases: ATATTTTCGATATCCACCA.
The two nucleotides/molecules that make up a connection are called a base pair. The rules to base pairs are…
Water is essential to life -- it has unique properties that almost all biological processes depend on.
Recall that...
Oxygen atoms are extremely electronegative, meaning that oxygen has the propensity to pull the buzzing/hopping electrons more around itself than the atoms it's bound to. As such, in a water molecule, the electrons will spend more time solely around the oxygen atom than they do the hydrogen atom or a position that binds the hydrogen and oxygen together. This is what gives the oxygen atom in a water molecule a weakly negative charge (as indicated by δ-) while the hydrogen atoms have a weakly positive charge (as indicated by δ+). These types of charged molecules are called polar molecules.
This weakly negative / weakly positive charge is what gives water several of the unique properties that biological properties depend on. Water molecules have a tendency to gravitate towards each other because the weakly negative oxygen atoms and the weakly positive hydrogen atoms of different water molecules attract. This attraction is called a hydrogen bond. Hydrogen bonds are weaker than covalent bonds in that the bonds aren't really solid -- water molecules can easily break off and go past each other.
The weak attraction between water molecules is also what makes water a solvent. So long as they're polar molecules, other molecules can travel inside of water using the same attraction from weakly negative / weakly positive charges -- they gravitate and float around water molecules just as other water molecules do. For example, the cytoplasm of a cell is a solvent (mostly water). It works because other molecules in the cytoplasm (e.g. cellular machinery) can float around / travel around using the weakly negative / weakly positive charges.
Water is called a universal solvent because it can dissolve more molecules than other other liquid. Note that the term universal doesn't mean that it can dissolve everything, just that it can dissolve more things than the others.
The properties that make water conducive for biological processes to operate:
Other terminology related to water:
Cells are the basic unit of living things / the building blocks of life. They're tiny structures that encapsulate information and machinery that allows them to replicate/reproduce and perform other important functions (e.g. appendages to move around).
There are 2 types of cells: eukaryotic and prokaryotic. There main differences between them are that...
Other differences between eukaryotes and prokaryotes ...
| Eukaryotes | Prokaryotes | |
|---|---|---|
| Size | 10 to 100 micrometers (μm) | 0.1 to 5 micrometers (μm) |
| Complexity | More complex | More simple |
| Sub-compartments (organelles) | Yes | No |
| DNA layout | Multiple stands | Single circular strand |
| Single-cell organisms | Yes (e.g. amoeba) | Yes (e.g. bacteria and archaea) |
| Multi-cell organisms | Yes (e.g. animals and fungus) | No |
Different cell species vary in features. The subsections below detail common cell features (not exhaustive).
Some features are only present in certain cell speicies (e.g. only some cells have a flagellum tail) while other features are present in all cells but in different amounts (e.g. every cell has cytosol but larger cells have more cytosol).
The cytoplasm (both eukaryotic and prokaryotic) is the insides/guts of a cell. Cytosol refers to just the fluid, while cytoplasm refers to fluid as well as everything else inside the cell.
The plasma membrane (present in both eukaryotic and prokaryotic cells) is the thing encapsulating the cytoplasm. It's what keeps the guys of the cell inside and controls the movement of substances coming into / going out of the cytoplasm.
Every cell has a membrane encapsulating its cytoplasm. Membranes in general follow the fluid mosaic model.
The term membrane can refer to either the plasma membrane or the membrane of a eukaryotic cell's organelle. How you should interpret it depends on the context in which its used.
The cell wall (present in both eukaryotic and prokaryotic cells) is a stiff layer around the membrane meant for protection. Not all cells have a cell wall -- for example, animal cells don't but plant cells do. Technically, the cell wall (if it exists) isn't considered to be part of the cell. The membrane and everything in it is.
The material states that cell walls...
Almost all prokaryotes have cell walls. Only some eukaryotes have cell walls (e.g. fungi and plants). The material says that cell walls for most bacteria are made up of a molecule called peptidoglycan, but it can be different for other cells. For example, this link says that plant cells have cell walls made up of cellulose.
The Capsule (present in prokaryotic cell only) is the outermost layer of some types of cells (typically bacteria cells). Capsules are made up of carbohydrates and there mainly to help the cell stick itself to the environment.
Ribosome (present in both eukaryotic and prokaryotic cells) are tiny molecular machines inside the cytoplasm that take in mRNA molecules (portions of DNA that have been written out) and produce proteins. Ribosomes themselves are structures made of proteins and RNA.
Ribosomes can either be floating around in the cytoplasm (called free ribosome) or be embedded in the membrane of endoplasmic reticulum.
Some cells have appendages that help them move (or stay put). There are different types of appendages...
Eukaryotic cells are typically larger and have membrane-bound sub-compartments, called organelles, that hold in the guts of different regions of the cell. For example, their DNA is encapsulated in a organelle called the nucleus.
Eukaryotes have their DNA broken up into multiple strands. They can either be single-cellular organisms (e.g. amoeba) or multi-cellular organisms (e.g. human). Single-cellular organism that are eukaryotic are called protists.
The following are descriptions for some of the organelles shown in the diagram above.
Nucleus is an organelle that contains DNA (genetic information required for the functioning and replication). Both prokaryotic and eukaryotic cells have DNA, but only eukaryotic cells have a nucleus. In prokaryotic cells, the DNA flows around freely instead of being encapsulated in a nucleus.
Most eukaryotic cells contain a single nucleus, but some contain can have 0 and others can have more than one. An example of 0 is blood cells -- mature blood cells don't have any DNA, therefore no nucleus. An example of more than 1 is the organism Oxytricha trifillax -- it contains 2 nuclei, each containing different DNA (its DNA is fragmented across 2 nuclei).
Endoplasmic Reticulum is layered membrane (organelle?) that surrounds the nucleus and is directly connected to pores on the nucleus. Large portions of the endoplasmic reticulum's membrane have ribosomes attached. The parts that have ribosomes attached are called rough endoplasmic reticulum while the parts that don't are called smooth endoplasmic reticulum.
Recall that ribosomes are what translate mRNA to proteins. Since the endoplasmic reticulum is directly connected to the nucleus (via pores on the nucleus), it provides a fairly straight-forward path for protein generation: mRNA produced in the nucleus...
Golgi are layered membrane (organelle?) that look similar to rough endoplasmic reticulum but aren't attached to the nucleus. Golgi package moleculues (e.g. proteins) for travel to either another part of the cell or outside of the cell. They do this by pinching off parts of their membrane to wrap around the molecule.
They're also responsible for building lysosomes (cell digestion machines).
Mitochondria are organelles responsible for cellular respiration: the process of producing Adenosine Triphosphate (ATP) from molecules such as sugars. ATP is a chemical that provides energy to drive various biological processes (e.g. muscle contractions). As such, mitochondria are often referred to as "the power house of the cell."
The major parts of chloroplast are...
Mitochondria have their own independent DNA (different from the DNA in the nucleus). It's speculated that at some point in the past they may have been independent single-cell organisms that formed a symbiotic relationship with a larger cell by living in it, eventually becoming part of the cell (endosymbiosis).
Unlike how normal offspring DNA gets produced by mixing DNA from both parents, mitochondrial DNA comes entirely from the mother's side.
Lysosomes are organelles (animal cells only) that help break down waste products / foreign substances by containing various enzymes and maintaining an acidic pH. Lysosomes are more often found in animals cells than plant and algae cells.
Peroxisomes are organelles that are similar to Lysosomes -- both are small organelles that break down unwanted substances. The difference is that peroxisomes have different types of enzymes that require oxygen (oxidative enzymes).
Chloroplasts are organelle (only plant and algae cells) responsible for photosynthesis. Photosynthesis is the process of taking in light and using it to build sugars from carbon dioxide. Those sugars are then used by the mitochondria to produce energy in a process called cellular respiration.
The major parts of chloroplast are...
Like mitochondria, chloroplast have their own independent DNA (different from the DNA in the nucleus). It's speculated that at some point in the past they may have been independent single-cell organisms that formed a symbiotic relationship with a larger cell by living in it, eventually becoming part of the cell (endosymbiosis).
Vacuoles are organelle (mostly plant and algae cells) responsible for storage (water, food, waste?) and enzymes that help break things down. Vacuoles are typically found in plant and algae cells, but may also exist in animal cells. The ones in plants / algae tend to be much larger.
Vacuoles are often responsible for a plant's shape. For example, a well watered plant will be upright and spry because its vacuoles are full. A plant that isn't as well watered may be sagging down or wilting because the vacuoles are less full
Prokaryotic cells: These cells are typically smaller and don't have organelles. For example, their DNA is free-floating in the cell (it's free floating but stays mostly in the center area called the nucleoid).
Prokaryotes have a single circular-strand of DNA. They can only be single-cellular organisms (e.g. bacteria).
The fluid mosaic model is the accepted model for how cell membranes work. The model says that a cell membrane is composed of a phospholipid bilayer with proteins, lipids, and carbohydrates floating around on either side or embedded in between.
A phospholipid is a amphipathic lipid molecule that involves a phosphate group. The...
As such, phospholipids have a natural tendency to form as a phospholipid bilayer (2 layers attached together, called a liposome) or a ball (called a micelle). The hydrophilic heads are going to point towards the water causing the hydrophobic tails to point at each other.
How fluid a phospholipid bilayer is depends on the types of phospholipid molecules that make it up and the temperature. Phospholipid molecules have 2 fatty acid tails. The fatty acid tails can be either...
At cooler temperatures, phospholipids that have 2 saturated fatty acid tails (straight tails) tend to get more rigid / dense because they can more easily pack together. Phospholipids with unsaturated fatty acid tails (bent tails) don't end up getting as rigid / dense, allowing the membrane to stay fluid at lower temperatures. Cholestrol embedded in the phospholipid bilayer also helps it stay more fluid at lower temperatures.
Examples of molecules that can be embedded in or attached to the phospholipid bilayer include...
The first record of a cell was in 1665 when Robert Hooke published a book called The Micrographia. The book contains drawings of observations he made while looking at various dead organisms through a rudimentary microscope.
A few years later, a Dutch lenscrafter by the name of Antonie Van Leeuwenhoek decided to use his expertise to craft a better microscope to better observe living cells / organisms. For example, he was able to observe sperm and Protists (unicellular organisms while he dubbed animalcules).
In the 1830s, Matthias Schleiden and Theodore Schwann began laying the groundwork for modern cell theory. They came up with the idea that...
They also suspected that cells come from other cells, but didn't know for sure if that was the only way they were produced. It was Robert Remak that in the mid-1800s established that...
It's still an open question as to how the first / initial cell came to be. The current working theory is that, 3.5 billion years ago, phospholipids (the molecules that form the membrane of a cell) naturally form bilayers and connect in a circle. A membrane may have naturally encapsulated a set of arbitrary self-replication molecules (e.g. protein or RNA) and that's how the first cell began growing and splitting off.
An enzyme is a molecule that takes in a specific set of input molecules and transforms them into a specific set of output molecules by putting those molecules in an environment that's favourable for chemical reactions to take place. The transformation takes the inputs and either ...
An enzyme is almost always a protein molecule but can also be a RNA-like molecule called a ribozyme.
The general terminology for enzymes are as follows:
Enzymes have a limited set of substrate types that they accept. A substrate will bind to the active site of the enzyme only if it fits into the active site. For example, the following diagram shows 2 substrates binding to an enzyme, the enzyme facilitating their their assembly, then releasing back out.
There was previously a thought that enzymes had a “lock-and-key” model, similar to how puzzle pieces fit together. Later on it was found out that an enzymes actually induce fit by changing shape slightly when they bind with substrates, such that they can better hold on to those substrates.
Examples of enzymes and what they do:
A metabolic pathway is a network/graph of enzymes that produces a final resulting molecule. Each enzyme produces molecules that feed into other enzymes in the pathway, eventually forming the final molecule. The term intermediate refers to an output of one enzyme that’s used as an input by another.
For example, the following graph is the metabolic pathway for gamma-hydroxybutyric acid...
Metabolism can be broken down into 2 categories: anabolism (building-up) and catabolism (breaking-down).
The process that builds up a molecule from smaller molecules is called anabolism. An enzyme takes in the molecules and creates bonds between them via an endergonic reactions: energy is stored as bonds between the smaller molecules thereby forming the larger molecule.
An example of anabolism is photosynthesis: plants will bond carbon dioxide gas () with water () using energy from the sun, creating sugar ()
Metabolism can be broken down into 2 categories: anabolism (building-up) and catabolism (breaking-down).
The process that breaks down a large molecule into smaller molecules is called catabolism. An enzyme takes in a larger molecule breaks up some of its bonds via exergonic rections: energy used as bonds in the molecule are release thereby breaking it up into smaller molecules.
An example of catabolism is cellular respiration: cells will break down the bonds in glucose () to release energy, splitting into carbon dioxide () and water ()
Adenosine Triphosphate (ATP) is a molecule that provides energy to drive various biological processes (e.g. muscle contractions). The third phosphoral group at the very end has a high-energy bond. When broken, energy is released and the resulting molecules are the broken up phosphoral group and Adenosine Diphosphate (ADP).
ATP is produced in the mitochondria. Similar to how the mitochondria is refered to as the powerhouse of the cell, ATP is often referred to as the energy currency of the cell / energy store for the cell.
Microscopes are devices used to magnify (zoom in) on objects, such that you can see things that you normally would be too small to see on your own. The term microscope comes from the words...
A picture taken through a microscope is called a micrograph. The distinguishing factors for most microscopes or the amount of magnification and the resolution of the output image.
There are different types of microscopes:
Terminology that's relevant but doesn't fit in any other section goes here.
Density - The mass per unit volume of a substance.
Specific heat capacity - The amount of heat needed to raise the temperature of one gram of a substance by one degree Celsius.
Heat of vaporization - The amount of energy needed to change one gram of a liquid substance to a gas at constant temperature.
endosymbiosis - A form of symbosis where one organism lives inside of of the other (e.g. gut bacteria lives in our colon). The prefix endo means within.